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  <div class="section" id="plot">
<h1>plot<a class="headerlink" href="#plot" title="Permalink to this headline">¶</a></h1>
<div class="section" id="module-atomman.plot">
<span id="functions-and-attributes"></span><h2>Functions and attributes<a class="headerlink" href="#module-atomman.plot" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="atomman.plot.interpolate_contour">
<code class="sig-prename descclassname">atomman.plot.</code><code class="sig-name descname">interpolate_contour</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">name</em>, <em class="sig-param">property=None</em>, <em class="sig-param">index=None</em>, <em class="sig-param">magnitude=False</em>, <em class="sig-param">plotxaxis='x'</em>, <em class="sig-param">plotyaxis='y'</em>, <em class="sig-param">xlim=None</em>, <em class="sig-param">ylim=None</em>, <em class="sig-param">zlim=None</em>, <em class="sig-param">xbins=200</em>, <em class="sig-param">ybins=200</em>, <em class="sig-param">dots=True</em>, <em class="sig-param">czero=True</em>, <em class="sig-param">save=False</em>, <em class="sig-param">show=True</em>, <em class="sig-param">length_unit='angstrom'</em>, <em class="sig-param">property_unit=None</em>, <em class="sig-param">cmap='jet'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.plot.interpolate_contour" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates a contour plot of a system’s per-atom properties by interpolating
properties between atoms.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system with the per-atom property that you want to plot.</p></li>
<li><p><strong>name</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The name of the per-atom property that you want to plot.</p></li>
<li><p><strong>property</strong> (<em>array-like object</em><em>, </em><em>optional</em>) – Values for the per-atom property to plot.  If not given, values will
be taken as the “name” property of system.</p></li>
<li><p><strong>index</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – Specifies which component of a multidimensional property to plot.  Not
needed if the property is scalar.</p></li>
<li><p><strong>magnitude</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, plots the per-atom magnitude of a vector property.  Cannot be
combined with index.  Default value is False.</p></li>
<li><p><strong>plotxaxis</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>array-like object</em><em>, </em><em>optional</em>) – Indicates the Cartesian direction associated with the system’s atomic
coordinates to align with the plotting x-axis.  Values are either 3D
unit vectors, or strings ‘x’, ‘y’, or ‘z’ for the Cartesian axes
directions.  plotxaxis and plotyaxis must be orthogonal.  Default value
is ‘x’ = [1, 0, 0].</p></li>
<li><p><strong>plotyaxis</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>array-like object</em><em>, </em><em>optional</em>) – Indicates the Cartesian direction associated with the system’s atomic
coordinates to align with the plotting y-axis.  Values are either 3D
unit vectors, or strings ‘x’, ‘y’, or ‘z’ for the Cartesian axes
directions.  plotxaxis and plotyaxis must be orthogonal.  Default value
is ‘y’ = [0, 1, 0].</p></li>
<li><p><strong>xlim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – The minimum and maximum coordinates along the plotting x-axis to
include in the fit.  Values are taken in the specified length_unit.
If not given, then the limits are set based on min and max atomic
coordinates along the plotting axis.</p></li>
<li><p><strong>ylim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – The minimum and maximum coordinates along the plotting y-axis to
include in the fit.  Values are taken in the specified length_unit.
If not given, then the limits are set based on min and max atomic
coordinates along the plotting axis.</p></li>
<li><p><strong>zlim</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – The minimum and maximum coordinates normal to the plotting axes
(i.e. plotxaxis X plotyaxis) to include in the fit.  Values are taken
in the specified length_unit.  If not given, then the limits are set
based on min and max atomic coordinates along the axis.</p></li>
<li><p><strong>xbins</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – Specifies the number of interpolation bins to use along the plotting
x-axis.  Default value is 200.</p></li>
<li><p><strong>ybins</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – Specifies the number of interpolation bins to use along the plotting
y-axis.  Default value is 200.</p></li>
<li><p><strong>dots</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, then the positions of the atoms are shown as circles.
Default value is True.</p></li>
<li><p><strong>czero</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, the range of property values will be centered around zero,
i.e. cmax = -cmin.  If False, cmax and cmin will be independently
selected using the property values.  Default value is True.</p></li>
<li><p><strong>save</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, the generated plot will be saved to “name.png”.  Default
value is False.</p></li>
<li><p><strong>show</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, matplotlib.pyplot.show() is called.  Default value is True.</p></li>
<li><p><strong>length_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The units of length to use for the plotting x- and y-axes.  Default
value is ‘angstrom’.</p></li>
<li><p><strong>property_unit</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><a class="reference external" href="https://docs.python.org/3/library/constants.html#None" title="(in Python v3.9)"><em>None</em></a><em>, </em><em>optional</em>) – The units to use for the property value being plotted.  Default value
is None, in which no unit conversion is applied.</p></li>
<li><p><strong>cmap</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – The name of the matplotlib colormap to use.  Default value is ‘jet’.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>intsum</strong> (<em>float</em>) – The area integrated sum of the property over the plotted region.</p></li>
<li><p><strong>avsum</strong> (<em>float</em>) – The average property value taken across all plotting bins.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

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  <h3><a href="index.html">Table of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">plot</a><ul>
<li><a class="reference internal" href="#module-atomman.plot">Functions and attributes</a></li>
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